The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

(2014) Alice Pajoro et al.   GENOME BIOLOGY

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

(2013) Ralph Stadhouders et al.   Nature Protocols

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Gene networks controllingArabidopsis thalianaflower development

(2013) Diarmuid Seosamh Ó'Maoiléidigh et al.   NEW PHYTOLOGIST

Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS

(2013) D. S. O'Maoileidigh et al.   PLANT CELL

MADS Domain Transcription Factors Mediate Short-Range DNA Looping That Is Essential for Target Gene Expression in Arabidopsis

(2013) M. A. Mendes et al.   PLANT CELL

Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis

(2013) K. E. Jaeger et al.   PLANT CELL

Gibberellins accumulate in the elongating endodermal cells of Arabidopsis root

(2013) E. Shani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana

(2013) R. Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flowering time regulation: photoperiod- and temperature-sensing in leaves

(2013) Young Hun Song et al.   TRENDS IN PLANT SCIENCE

Forecasting flowering phenology under climate warming by modelling the regulatory dynamics of flowering-time genes

(2013) Akiko Satake et al.   Nature Communications

Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana

(2013) Nora Bujdoso et al.   Frontiers in Plant Science

Transcription factors on the move

(2012) Shuang Wu et al.   CURRENT OPINION IN PLANT BIOLOGY

Spatially distinct regulatory roles for gibberellins in the promotion of flowering of Arabidopsis under long photoperiods

(2012) A. Porri et al.   DEVELOPMENT

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

(2012) C. Smaczniak et al.   DEVELOPMENT

Spatial control of flowering by DELLA proteins in Arabidopsis thaliana

(2012) V. C. Galvao et al.   DEVELOPMENT

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses

(2012) Eunkyoo Oh et al.   NATURE CELL BIOLOGY

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Arabidopsis Shoot Meristem Transcriptome during Floral Transition Identifies Distinct Regulatory Patterns and a Leucine-Rich Repeat Protein That Promotes Flowering

(2012) S. Torti et al.   PLANT CELL

Gibberellin Regulates the Arabidopsis Floral Transition through miR156-Targeted SQUAMOSA PROMOTER BINDING-LIKE Transcription Factors

(2012) S. Yu et al.   PLANT CELL

Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis

(2012) Zhen Tao et al.   PLANT JOURNAL

Characterization of SOC1's Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators

(2012) R. G. H. Immink et al.   PLANT PHYSIOLOGY

Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA

(2012) S. E. Wuest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

(2012) C. Smaczniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

The end of innocence: flowering networks explode in complexity

(2011) David Posé et al.   CURRENT OPINION IN PLANT BIOLOGY

LATE MERISTEM IDENTITY2 acts together with LEAFY to activate APETALA1

(2011) J. J. Pastore et al.   DEVELOPMENT

LEAFY Target Genes Reveal Floral Regulatory Logic, cis Motifs, and a Link to Biotic Stimulus Response

(2011) Cara M. Winter et al.   DEVELOPMENTAL CELL

Heterologous Expression of the Chrysanthemum R2R3-MYB Transcription Factor CmMYB2 Enhances Drought and Salinity Tolerance, Increases Hypersensitivity to ABA and Delays Flowering in Arabidopsis thaliana

(2011) Hong Shan et al.   MOLECULAR BIOTECHNOLOGY

Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for theArabidopsisLEAFY Transcription Factor

(2011) Edwige Moyroud et al.   PLANT CELL

Mobile Gibberellin Directly StimulatesArabidopsisHypocotyl Xylem Expansion

(2011) Laura Ragni et al.   PLANT CELL

Uncovering genetic and molecular interactions among floral meristem identity genes in Arabidopsis thaliana

(2011) Valentina Grandi et al.   PLANT JOURNAL

The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis

(2011) Jae-Hoon Jung et al.   PLANT JOURNAL

GIGANTEA directly activates Flowering Locus T in Arabidopsis thaliana

(2011) M. Sawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis

(2011) W. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continuous-time modeling of cell fate determination in Arabidopsis flowers

(2010) Simon van Mourik et al.   BMC Systems Biology

Ovule development in Arabidopsis: progress and challenge

(2010) Dong-Qiao Shi et al.   CURRENT OPINION IN PLANT BIOLOGY

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

Regulation of transcription in plants: mechanisms controlling developmental switches

(2010) Kerstin Kaufmann et al.   NATURE REVIEWS GENETICS

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Hormone Profiling in Developing Arabidopsis Seeds: Examination of the Site of ABA Biosynthesis, ABA Transport and Hormone Interactions

(2010) Yuri Kanno et al.   PLANT AND CELL PHYSIOLOGY

Orchestration of the Floral Transition and Floral Development in Arabidopsis by the Bifunctional Transcription Factor APETALA2

(2010) L. Yant et al.   PLANT CELL

cis-Regulatory Elements and Chromatin State Coordinately Control Temporal and Spatial Expression of FLOWERING LOCUS T in Arabidopsis

(2010) J. Adrian et al.   PLANT CELL

Orchestration of Floral Initiation by APETALA1

(2010) K. Kaufmann et al.   SCIENCE

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

(2009) Stefanie De Bodt et al.   BMC GENOMICS

Prediction of Photoperiodic Regulators from Quantitative Gene Circuit Models

(2009) José Domingo Salazar et al.   CELL

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis

(2009) Gang Wu et al.   CELL

The MicroRNA-Regulated SBP-Box Transcription Factor SPL3 Is a Direct Upstream Activator of LEAFY, FRUITFULL, and APETALA1

(2009) Ayako Yamaguchi et al.   DEVELOPMENTAL CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins

(2009) Rainer Melzer et al.   NUCLEIC ACIDS RESEARCH

Global Identification of Targets of the Arabidopsis MADS Domain Protein AGAMOUS-Like15

(2009) Y. Zheng et al.   PLANT CELL

Crosstalk between Cold Response and Flowering in Arabidopsis Is Mediated through the Flowering-Time Gene SOC1 and Its Upstream Negative Regulator FLC

(2009) E. Seo et al.   PLANT CELL

The Arabidopsis floral meristem identity genes AP1, AGL24 and SVP directly repress class B and C floral homeotic genes

(2009) Veronica Gregis et al.   PLANT JOURNAL

Genetic and spatial interactions betweenFT,TSFandSVPduring the early stages of floral induction in Arabidopsis

(2009) Seonghoe Jang et al.   PLANT JOURNAL

The ‘ABC’ of MADS domain protein behaviour and interactions

(2009) Richard G.H. Immink et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Floral organ identity: 20 years of ABCs

(2009) Barry Causier et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

From ABC genes to regulatory networks, epigenetic landscapes and flower morphogenesis: Making biological sense of theoretical approaches

(2009) Elena R. Alvarez-Buylla et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

(2009) Kerstin Kaufmann et al.   PLOS BIOLOGY

Repression of Flowering by the miR172 Target SMZ

(2009) Johannes Mathieu et al.   PLOS BIOLOGY

SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

(2009) Richard GH Immink et al.   GENOME BIOLOGY

Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis

(2008) C. Liu et al.   DEVELOPMENT

A Repressor Complex Governs the Integration of Flowering Signals in Arabidopsis

(2008) Dan Li et al.   DEVELOPMENTAL CELL

The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis

(2008) Stefan Schwarz et al.   PLANT MOLECULAR BIOLOGY